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- PDB-6gsn: Structure of a partial yeast 48S preinitiation complex in closed ... -

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Entry
Database: PDB / ID: 6gsn
TitleStructure of a partial yeast 48S preinitiation complex in closed conformation
Components
  • (40S ribosomal protein ...) x 17
  • (Eukaryotic translation initiation factor ...) x 10
  • 18S rRNA (1798-MER)
  • 60S ribosomal protein L41-A
  • KLLA0A07194p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B06182p
  • KLLA0B08173p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E12277p
  • KLLA0E23673p
  • KLLA0F07843p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • RPS23
  • Ubiquitin-40S ribosomal protein S27a
  • mRNA
  • tRNAi (75-MER)
KeywordsRIBOSOME / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / tRNAi / 48S PIC / small ribosome subunit
Function / homology
Function and homology information


formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex ...formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor binding / translation initiation factor activity / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / double-stranded RNA binding / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A ...Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S7e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / METHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit G ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / METHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta / Small ribosomal subunit protein eS32A / Eukaryotic translation initiation factor 2 subunit alpha / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit gamma / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 1A / Eukaryotic translation initiation factor 3 subunit I / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / RPS23 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.75 Å
AuthorsLlacer, J.L. / Hussain, T. / Ramakrishnan, V.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Citation
Journal: Nucleic Acids Res / Year: 2021
Title: Large-scale movement of eIF3 domains during translation initiation modulate start codon selection.
Authors: Jose L Llácer / Tanweer Hussain / Jinsheng Dong / Laura Villamayor / Yuliya Gordiyenko / Alan G Hinnebusch /
Abstract: The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single ...The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.
#1: Journal: Mol Cell / Year: 2015
Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan /
Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.
History
DepositionJun 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection
Category: em_admin / em_map ...em_admin / em_map / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _em_admin.last_update / _em_map.contour_level ..._em_admin.last_update / _em_map.contour_level / _em_map.contour_level_source / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / em_admin / em_map / pdbx_database_proc / pdbx_seq_map_depositor_info / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_map.file / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.4Nov 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: em_admin / em_entity_assembly_naturalsource / pdbx_entry_details
Item: _em_admin.last_update / _em_entity_assembly_naturalsource.id

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Assembly

Deposited unit
2: 18S rRNA (1798-MER)
C: KLLA0F09812p
D: KLLA0D08305p
F: KLLA0D10659p
K: KLLA0B08173p
M: 40S ribosomal protein S12
P: KLLA0F07843p
Q: 40S ribosomal protein S16
R: KLLA0B01474p
S: KLLA0B01562p
T: KLLA0A07194p
U: KLLA0F25542p
Z: KLLA0B06182p
c: 40S ribosomal protein S28
f: Ubiquitin-40S ribosomal protein S27a
g: KLLA0E12277p
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
h: 60S ribosomal protein L41-A
3: mRNA
i: Eukaryotic translation initiation factor 1A
m: Eukaryotic translation initiation factor eIF-1
o: Eukaryotic translation initiation factor 3 subunit A,eIF3a
q: Eukaryotic translation initiation factor 3 subunit C
k: Eukaryotic translation initiation factor 2 subunit gamma
l: Eukaryotic translation initiation factor 2 subunit beta
j: Eukaryotic translation initiation factor 2 subunit alpha
1: tRNAi (75-MER)
A: 40S ribosomal protein S0
B: 40S ribosomal protein S1
E: 40S ribosomal protein S4
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: KLLA0E23673p
L: KLLA0A10483p
N: KLLA0F18040p
O: 40S ribosomal protein S14
V: 40S ribosomal protein S21
W: 40S ribosomal protein S22
Y: 40S ribosomal protein S24
X: RPS23
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
p: Eukaryotic translation initiation factor 3 subunit B
s: Eukaryotic translation initiation factor 3 subunit I
r: Eukaryotic translation initiation factor 3 subunit G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,543,510134
Polymers1,540,61047
Non-polymers2,90187
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 231

#1: RNA chain 18S rRNA (1798-MER)


Mass: 579239.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: GenBank: 49642208
#20: RNA chain mRNA


Mass: 4321.563 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#28: RNA chain tRNAi (75-MER)


Mass: 24223.482 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 176433

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Protein , 16 types, 16 molecules CDFKPRSTUZfgJLNX

#2: Protein KLLA0F09812p


Mass: 23162.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKL3
#3: Protein KLLA0D08305p


Mass: 24830.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRK7
#4: Protein KLLA0D10659p


Mass: 22912.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRA3
#5: Protein KLLA0B08173p


Mass: 11423.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CVZ5
#7: Protein KLLA0F07843p


Mass: 13220.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKV4
#9: Protein KLLA0B01474p


Mass: 14886.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWU3
#10: Protein KLLA0B01562p


Mass: 16953.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWT9
#11: Protein KLLA0A07194p


Mass: 15747.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXM0
#12: Protein KLLA0F25542p


Mass: 12032.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CIM1
#13: Protein KLLA0B06182p


Mass: 7939.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW78
#15: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 7958.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P69061
#16: Protein KLLA0E12277p


Mass: 35612.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNI7
#35: Protein KLLA0E23673p


Mass: 20882.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM18
#36: Protein KLLA0A10483p


Mass: 17712.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CX80
#37: Protein KLLA0F18040p


Mass: 16858.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CJK0
#42: Protein RPS23


Mass: 15916.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q875M3

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40S ribosomal protein ... , 17 types, 17 molecules MQcdeABEGHIOVWYab

#6: Protein 40S ribosomal protein S12


Mass: 12710.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CLU4
#8: Protein 40S ribosomal protein S16


Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q875N2
#14: Protein 40S ribosomal protein S28 / S33


Mass: 6972.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P33285
#17: Protein 40S ribosomal protein S29


Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CPG3
#18: Protein 40S ribosomal protein S30


Mass: 6608.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CUH5
#29: Protein 40S ribosomal protein S0


Mass: 24368.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CN12
#30: Protein 40S ribosomal protein S1


Mass: 26404.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWD0
#31: Protein 40S ribosomal protein S4


Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWJ2
#32: Protein 40S ribosomal protein S6


Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM04
#33: Protein 40S ribosomal protein S7


Mass: 21033.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CTD6
#34: Protein 40S ribosomal protein S8


Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CMG3
#38: Protein 40S ribosomal protein S14 / RP59


Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P27069
#39: Protein 40S ribosomal protein S21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXT6
#40: Protein 40S ribosomal protein S22


Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW21
#41: Protein 40S ribosomal protein S24


Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CU44
#43: Protein 40S ribosomal protein S26


Mass: 11166.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CS01
#44: Protein 40S ribosomal protein S27


Mass: 8753.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNL2

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Protein/peptide , 1 types, 1 molecules h

#19: Protein/peptide 60S ribosomal protein L41-A / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P0CX86

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Eukaryotic translation initiation factor ... , 10 types, 10 molecules imoqkljpsr

#21: Protein Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 12659.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38912
#22: Protein Eukaryotic translation initiation factor eIF-1 / Protein translation factor SUI1


Mass: 10299.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUI1, RFR1, YNL244C, N0905 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32911
#23: Protein Eukaryotic translation initiation factor 3 subunit A,eIF3a / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / ...eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / Translation initiation factor eIF3 / p110 subunit homolog


Mass: 62822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38249
#24: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport ...eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 80545.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32497
#25: Protein Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 47230.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32481
#26: Protein Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 16458.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09064
#27: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 30221.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20459
#45: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation ...eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation initiation factor eIF3 p90 subunit


Mass: 76738.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PRT1, CDC63, YOR361C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06103
#46: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit homolog / eIF-3 39 kDa subunit homolog


Mass: 38229.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF34, SCY_4321 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZMK5, UniProt: P40217*PLUS
#47: Protein/peptide Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Translation initiation factor eIF3 p33 subunit homolog / eIF3 p33 homolog


Mass: 5576.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF35, SCY_1313 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZZ25

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Non-polymers , 4 types, 87 molecules

#48: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 81 / Source method: obtained synthetically / Formula: Mg
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#50: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#51: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S

-
Details

Has protein modificationN

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of a partial yeast 48S preinitiation complex in closed conformationRIBOSOME#1-#470MULTIPLE SOURCES
2RibosomeORGANELLE OR CELLULAR COMPONENT#1-#19, #29-#441NATURAL
3tRNACOMPLEX#281NATURAL
4Initiation factorsCOMPLEX#23-#27, #45-#471RECOMBINANT
5mRNACOMPLEX#201RECOMBINANT
6Initiation factorsCOMPLEX#21-#221RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)284590
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
45Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
56Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
24Saccharomyces cerevisiae (brewer's yeast)4932
36Escherichia coli BL21(DE3) (bacteria)469008
45synthetic construct (others)32630
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 mMMES1
28 mMMagnessium acetate1
340 mMPotassium acetate1
410 mMAmmonium acetate1
52 mMDithiothreitol (DTT)1
60.25 mMGDPCP1
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 32 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 5500
Details: Images were collected in movie-mode at 32 frames per second

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Processing

EM software
IDNameVersionCategory
2EMANparticle selection
3EPUimage acquisition
5CTFFIND3CTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1182309
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12586 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: FSC

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